Objectives: Following bone marrow transplantation (BMT), life expectancy of many patients increases , necessitating medical follow up, especially function of the endocrine gland. Previous studies have showed endocrine dysfunctions are caused not only by total body irradiation, but also by cytotoxic drug conditioning regimens. Materials and Methods: 46 patients (12 F, 34 M), aged 1.5-49 years were evaluated for thyroid (T3, T4, TSH, T3RU, FTI, Anti Tg-Ab, Anti TPO-Ab), parathyroid (Ca, Alkp, PTH), gonad function (LH, FSH, E2, progesterone in females and semen analysis in males) and function of β-cells of pancreas by O.G.T.T (in 12 major thalassemic patients) before and 3, 6, 12, 24 months after B.M.T, by the “Little” Busulfan-cyclophosphamide conditioning regimen. Results: There are no differences between results of clinical examinations and laboratory, tests of pre and post B.M.T function of thyroid or parathyroid and calcium metabolism. The function of leydig cells was normal in 11 adult men (G5P5) before and 3, 6, 12 months after B.M.T, but injury of germinal cells (oligo or azo spermia) before and 12 months after B.M.T was seen. There is no relation between FSH and injury of germinal cells. Development of puberty was normal in 5 boys (G2P2 or G3P3) before and one year after B.M.T. primary hypogonadism was induced in 4 females (B5P5) after B.M.T. In one 14 year-old female, regular menstruation continued 2 years after B.M.T. In one girl (P1B1 before BMT) ovarian failure developed 12 months after BMT. Function of β-cells in thalassemic patients (Ferritin>1000 before BMT) before and after BMT was normal. Conclusion: One year after B.M.T, only the chemotherapy conditioning regimen did not affect function of thyroid or parathyroid gland, but ovarian failure and germinal cells injuries developed (without effect on leydig cell). BMT had no effect on the function of β-cells of pancreas.